To register the sky-subtracted images to a common reference, it is
necessary to precisely estimate the offsets between them. jitter
applies a 2d cross-correlation routine to determine the offsets to an
accuracy of 1/10th of a pixel. There are other ways to find out
offsets between frames: with many point-sources, point-pattern
matching is a possibility. Identifying the same objects in all
consecutive frames would also yield a list of offsets between
frames. An initial estimate of the offsets between frames can be found
in the FITS headers. jitter assumes that the offsets found in
the input FITS headers have a certain accuracy. If there are no input
offsets, they are all initially estimated to be zero in both
directions.

Registering the images is done by resampling them with subpixel shifts
to align them all to a common reference (usually the first frame).
Resampling can make use of any interpolation algorithm, but be aware that
using cheap and dirty algorithms like nearest-neighbor or linear
interpolation can degrade the images by introducing aliasing. jitter
offers many higher-order interpolation kernels that introduce few or no
artifacts; however, the noise (high frequencies) will be smoothed a little
bit.

Stacking the resulting images is done using a 3d filter to remove
outliers and jitter gives you a choice between 3 different
filters. Linear means that all frames are actually averaged
without filtering (pass-all filter). This is not recommended as this
is likely to keep cosmic rays and other outliers in the final
frame. Median means that the final frame is the median of all
resampled frames. The last filter (default) scales all frames by their
medians and removes the highest and lowest pixel values before taking
an average. See the jitter documentation for more information.

Notice that in versions later than eclipse version 4, jitter
resamples and stacks in one step to speed up the process. Also
added since version 4, the final frame is a union of all input images
(as opposed to an intersection for previous versions), which means
that it is bigger than any of the initial input frames.